› 5nd8

Electron Microscopy
3.7Å resolution

Hibernating ribosome from Staphylococcus aureus (Unrotated state)

Released:
DOI: 10.2210/pdb5nd8/pdb
PDB entry 5nd8 coloured by chain, front view.
PDB entry 5nd8 coloured by chain, side view.
PDB entry 5nd8 coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
Primary publication:
Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF.
Khusainov I, Vicens Q, Ayupov R, Usachev K, Myasnikov A, Simonetti A, Validov S, Kieffer B, Yusupova G, Yusupov M, Hashem Y
EMBO J 36 2073-2087 (2017)
PMID: 28645916
Related structures: EMD-3624

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 52-mer (preferred)
PDBe Complex ID:
PDB-CPX-108479 (preferred)
Entry contents:
49 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (52 distinct):
Small ribosomal subunit protein uS2 Chain: b
Molecule details ›
Chain: b
Length: 255 amino acids
Theoretical weight: 29.14 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZ25 (Residues: 1-255; Coverage: 100%)
Gene names: SAOUHSC_01232, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS3 Chain: c
Molecule details ›
Chain: c
Length: 217 amino acids
Theoretical weight: 24.14 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW12 (Residues: 1-217; Coverage: 100%)
Gene names: SAOUHSC_02506, rpsC
Sequence domains:
Small ribosomal subunit protein uS4 Chain: d
Molecule details ›
Chain: d
Length: 200 amino acids
Theoretical weight: 23.05 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXK6 (Residues: 1-200; Coverage: 100%)
Gene names: SAOUHSC_01829, rpsD
Sequence domains:
Small ribosomal subunit protein uS5 Chain: e
Molecule details ›
Chain: e
Length: 166 amino acids
Theoretical weight: 17.77 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW23 (Residues: 1-166; Coverage: 100%)
Gene names: SAOUHSC_02494, rpsE
Sequence domains:
Small ribosomal subunit protein bS6 Chain: f
Molecule details ›
Chain: f
Length: 98 amino acids
Theoretical weight: 11.61 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2G113 (Residues: 1-98; Coverage: 100%)
Gene names: SAOUHSC_00348, rpsF
Sequence domains: Ribosomal protein S6
Small ribosomal subunit protein uS7 Chain: g
Molecule details ›
Chain: g
Length: 156 amino acids
Theoretical weight: 17.83 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: P48940 (Residues: 1-156; Coverage: 100%)
Gene names: SAOUHSC_00528, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS8 Chain: h
Molecule details ›
Chain: h
Length: 132 amino acids
Theoretical weight: 14.85 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW20 (Residues: 1-132; Coverage: 100%)
Gene names: SAOUHSC_02498, rpsH
Sequence domains: Ribosomal protein S8
Small ribosomal subunit protein uS9 Chain: i
Molecule details ›
Chain: i
Length: 132 amino acids
Theoretical weight: 14.86 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW39 (Residues: 1-132; Coverage: 100%)
Gene names: SAOUHSC_02477, rpsI
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 Chain: j
Molecule details ›
Chain: j
Length: 102 amino acids
Theoretical weight: 11.6 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: A7X5G6 (Residues: 1-102; Coverage: 100%)
Gene names: SAHV_2235, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS11 Chain: k
Molecule details ›
Chain: k
Length: 129 amino acids
Theoretical weight: 13.91 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW31 (Residues: 1-129; Coverage: 100%)
Gene names: SAOUHSC_02486, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein uS12 Chain: l
Molecule details ›
Chain: l
Length: 137 amino acids
Theoretical weight: 15.32 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: P0A0H0 (Residues: 1-137; Coverage: 100%)
Gene names: SAOUHSC_00527, rpsL
Sequence domains: Ribosomal protein S12/S23
Small ribosomal subunit protein uS13 Chain: m
Molecule details ›
Chain: m
Length: 121 amino acids
Theoretical weight: 13.75 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW30 (Residues: 1-121; Coverage: 100%)
Gene names: SAOUHSC_02487, rpsM
Sequence domains: Ribosomal protein S13/S18
Small ribosomal subunit protein uS14B Chain: n
Molecule details ›
Chain: n
Length: 61 amino acids
Theoretical weight: 7.32 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW19 (Residues: 1-61; Coverage: 100%)
Gene names: SAOUHSC_02499, rpsN1, rpsZ
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: o
Molecule details ›
Chain: o
Length: 89 amino acids
Theoretical weight: 10.63 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2G2Q1 (Residues: 1-89; Coverage: 100%)
Gene names: SAOUHSC_01250, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein bS16 Chain: p
Molecule details ›
Chain: p
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZ45 (Residues: 1-91; Coverage: 100%)
Gene names: SAOUHSC_01208, rpsP
Sequence domains: Ribosomal protein S16
Small ribosomal subunit protein uS17 Chain: q
Molecule details ›
Chain: q
Length: 87 amino acids
Theoretical weight: 10.2 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW15 (Residues: 1-87; Coverage: 100%)
Gene names: SAOUHSC_02503, rpsQ
Sequence domains: Ribosomal protein S17
Small ribosomal subunit protein bS18 Chain: r
Molecule details ›
Chain: r
Length: 80 amino acids
Theoretical weight: 9.33 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2G111 (Residues: 1-80; Coverage: 100%)
Gene names: SAOUHSC_00350, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS19 Chain: s
Molecule details ›
Chain: s
Length: 92 amino acids
Theoretical weight: 10.64 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW10 (Residues: 1-92; Coverage: 100%)
Gene names: SAOUHSC_02508, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein bS20 Chain: t
Molecule details ›
Chain: t
Length: 83 amino acids
Theoretical weight: 9.04 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXY6 (Residues: 1-83; Coverage: 100%)
Gene names: SAOUHSC_01689, rpsT
Sequence domains: Ribosomal protein S20
Small ribosomal subunit protein bS21 Chain: u
Molecule details ›
Chain: u
Length: 58 amino acids
Theoretical weight: 6.99 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXZ7 (Residues: 1-58; Coverage: 100%)
Gene names: SAOUHSC_01678, rpsU
Sequence domains: Ribosomal protein S21
Ribosome hibernation promotion factor Chain: v
Molecule details ›
Chain: v
Length: 190 amino acids
Theoretical weight: 22.24 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q2G055 (Residues: 1-190; Coverage: 100%)
Gene names: SAOUHSC_00767, hpf
Sequence domains:
Large ribosomal subunit protein uL2 Chain: D
Molecule details ›
Chain: D
Length: 277 amino acids
Theoretical weight: 30.22 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: P60430 (Residues: 1-277; Coverage: 100%)
Gene names: SAOUHSC_02509, rplB
Sequence domains:
Large ribosomal subunit protein uL3 Chain: E
Molecule details ›
Chain: E
Length: 220 amino acids
Theoretical weight: 23.76 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW06 (Residues: 1-220; Coverage: 100%)
Gene names: SAOUHSC_02512, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4 Chain: F
Molecule details ›
Chain: F
Length: 207 amino acids
Theoretical weight: 22.5 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW07 (Residues: 1-207; Coverage: 100%)
Gene names: SAOUHSC_02511, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein uL5 Chain: G
Molecule details ›
Chain: G
Length: 179 amino acids
Theoretical weight: 20.3 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW18 (Residues: 1-179; Coverage: 100%)
Gene names: SAOUHSC_02500, rplE
Sequence domains:
Large ribosomal subunit protein uL6 Chain: H
Molecule details ›
Chain: H
Length: 178 amino acids
Theoretical weight: 19.82 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW21 (Residues: 1-178; Coverage: 100%)
Gene names: SAOUHSC_02496, rplF
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL13 Chain: M
Molecule details ›
Chain: M
Length: 145 amino acids
Theoretical weight: 16.36 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW38 (Residues: 1-145; Coverage: 100%)
Gene names: SAOUHSC_02478, rplM
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL14 Chain: N
Molecule details ›
Chain: N
Length: 122 amino acids
Theoretical weight: 13.16 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW16 (Residues: 1-122; Coverage: 100%)
Gene names: SAOUHSC_02502, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL15 Chain: O
Molecule details ›
Chain: O
Length: 146 amino acids
Theoretical weight: 15.63 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: P0A0F8 (Residues: 1-146; Coverage: 100%)
Gene names: SAOUHSC_02492, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL16 Chain: P
Molecule details ›
Chain: P
Length: 144 amino acids
Theoretical weight: 16.27 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW13 (Residues: 1-144; Coverage: 100%)
Gene names: SAOUHSC_02505, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL17 Chain: Q
Molecule details ›
Chain: Q
Length: 122 amino acids
Theoretical weight: 13.77 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW33 (Residues: 1-122; Coverage: 100%)
Gene names: SAOUHSC_02484, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein uL18 Chain: R
Molecule details ›
Chain: R
Length: 119 amino acids
Theoretical weight: 13.12 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW22 (Residues: 1-119; Coverage: 100%)
Gene names: SAOUHSC_02495, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein bL19 Chain: S
Molecule details ›
Chain: S
Length: 116 amino acids
Theoretical weight: 13.39 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZ42 (Residues: 1-116; Coverage: 100%)
Gene names: SAOUHSC_01211, rplS
Sequence domains: Ribosomal protein L19
Large ribosomal subunit protein bL20 Chain: T
Molecule details ›
Chain: T
Length: 118 amino acids
Theoretical weight: 13.72 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXQ1 (Residues: 1-118; Coverage: 100%)
Gene names: SAOUHSC_01784, rplT
Sequence domains: Ribosomal protein L20
Large ribosomal subunit protein bL21 Chain: U
Molecule details ›
Chain: U
Length: 102 amino acids
Theoretical weight: 11.35 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXS8 (Residues: 1-102; Coverage: 100%)
Gene names: SAOUHSC_01757, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL22 Chain: V
Molecule details ›
Chain: V
Length: 117 amino acids
Theoretical weight: 12.86 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW11 (Residues: 1-117; Coverage: 100%)
Gene names: SAOUHSC_02507, rplV
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein uL23 Chain: W
Molecule details ›
Chain: W
Length: 91 amino acids
Theoretical weight: 10.63 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW08 (Residues: 1-91; Coverage: 100%)
Gene names: SAOUHSC_02510, rplW
Sequence domains: Ribosomal protein L23
Large ribosomal subunit protein uL24 Chain: X
Molecule details ›
Chain: X
Length: 105 amino acids
Theoretical weight: 11.56 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW17 (Residues: 1-105; Coverage: 100%)
Gene names: SAOUHSC_02501, rplX
Sequence domains:
Large ribosomal subunit protein bL25 Chain: Y
Molecule details ›
Chain: Y
Length: 217 amino acids
Theoretical weight: 23.81 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2G0S0 (Residues: 1-217; Coverage: 100%)
Gene names: SAOUHSC_00474, ctc, rplY
Sequence domains:
Large ribosomal subunit protein bL27 Chain: Z
Molecule details ›
Chain: Z
Length: 94 amino acids
Theoretical weight: 10.33 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXT0 (Residues: 1-94; Coverage: 100%)
Gene names: SAOUHSC_01755, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein bL28 Chain: 0
Molecule details ›
Chain: 0
Length: 62 amino acids
Theoretical weight: 7 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZ60 (Residues: 1-62; Coverage: 100%)
Gene names: SAOUHSC_01191, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: 1
Molecule details ›
Chain: 1
Length: 69 amino acids
Theoretical weight: 8.11 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW14 (Residues: 1-69; Coverage: 100%)
Gene names: SAOUHSC_02504, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL30 Chain: 2
Molecule details ›
Chain: 2
Length: 59 amino acids
Theoretical weight: 6.57 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: P0A0G2 (Residues: 1-59; Coverage: 100%)
Gene names: SAOUHSC_02493, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein bL31B Chain: 3
Molecule details ›
Chain: 3
Length: 84 amino acids
Theoretical weight: 9.74 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FWD8 (Residues: 1-84; Coverage: 100%)
Gene names: SAOUHSC_02361, rpmE2
Sequence domains: Ribosomal protein L31
Large ribosomal subunit protein bL32 Chain: 4
Molecule details ›
Chain: 4
Length: 58 amino acids
Theoretical weight: 6.66 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FZF1 (Residues: 1-58; Coverage: 100%)
Gene names: SAOUHSC_01078, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL33B Chain: 5
Molecule details ›
Chain: 5
Length: 49 amino acids
Theoretical weight: 5.89 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FY22 (Residues: 1-49; Coverage: 100%)
Gene names: SAOUHSC_01651, rpmG2
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein bL34 Chain: 6
Molecule details ›
Chain: 6
Length: 45 amino acids
Theoretical weight: 5.45 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FUQ0 (Residues: 1-45; Coverage: 100%)
Gene names: SAOUHSC_03055, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL35 Chain: 7
Molecule details ›
Chain: 7
Length: 66 amino acids
Theoretical weight: 7.72 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FXQ0 (Residues: 1-66; Coverage: 100%)
Gene names: SAOUHSC_01785, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL36 Chain: 8
Molecule details ›
Chain: 8
Length: 37 amino acids
Theoretical weight: 4.32 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
UniProt:
  • Canonical: Q2FW29 (Residues: 1-37; Coverage: 100%)
Gene names: SAOUHSC_02488, rpmJ
Sequence domains: Ribosomal protein L36
16S ribosomal RNA Chain: a
Molecule details ›
Chain: a
Length: 1547 nucleotides
Theoretical weight: 500.46 KDa
Sequence domains: Bacterial small subunit ribosomal RNA
23S ribosomal RNA Chain: A
Molecule details ›
Chain: A
Length: 2918 nucleotides
Theoretical weight: 945.06 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: B
Molecule details ›
Chain: B
Length: 114 nucleotides
Theoretical weight: 36.69 KDa
Sequence domains: 5S ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-3624
Expression system: Escherichia coli BL21

Quick links

Citations

6 review citations

Ribosome Hibernation.
Prossliner et al. (2018)
5 more

5 mentions without citation

Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF.
Khusainov et al. (2017)
4 more